ArticleJournal of clinical microbiology2022
External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.
Article in Journal of clinical microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- External quality assessment of molecular detection and variant typing of SARS-CoV-2 in European expert laboratories in 2023.Journal of clinical microbiology · 2025Article
- Observational
- How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?Microorganisms · 2024Article
- Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria.Frontiers in molecular biosciences · 2024Article
- A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2023Article
- Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting.Scientific reports · 2023Article
- FAIR+E pathogen data for surveillance and research: lessons from COVID-19.Frontiers in public health · 2023Article
- SARS-CoV-2 transmission dynamics in bars, restaurants, and nightclubs.Frontiers in microbiology · 2023Article
- Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories.Journal of clinical microbiology · 2022Article
- COVID-19 infection and transmission includes complex sequence diversity.PLoS genetics · 2022Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
- Increased transmissibility of SARS-CoV-2 alpha variant (B.1.1.7) in children: three large primary school outbreaks revealed by whole genome sequencing in the Netherlands.BMC infectious diseases · 2022Article
- Women in the European Virus Bioinformatics Center.Viruses · 2022Article
- SARS-CoV-2 Vaccine Alpha and Delta Variant Breakthrough Infections Are Rare and Mild but Can Happen Relatively Early after Vaccination.Microorganisms · 2022Article
Corrections and comments
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Authors and funding
52 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.
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